1LD9

THE THREE-DIMENSIONAL STRUCTURE OF AN H-2LD PEPTIDE COMPLEX EXPLAINS THE UNIQUE INTERACTION OF LD WITH BETA2M AND PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The three-dimensional structure of an H-2Ld-peptide complex explains the unique interaction of Ld with beta-2 microglobulin and peptide.

Balendiran, G.K.Solheim, J.C.Young, A.C.Hansen, T.H.Nathenson, S.G.Sacchettini, J.C.

(1997) Proc.Natl.Acad.Sci.USA 94: 6880-6885


  • PubMed Abstract: 
  • Solution at 2.5-A resolution of the three-dimensional structure of H-2Ld with a single nine-residue peptide provides a structural basis for understanding its unique interaction with beta-2 microglobulin (beta2m) and peptide. Consistent with the biolo ...

    Solution at 2.5-A resolution of the three-dimensional structure of H-2Ld with a single nine-residue peptide provides a structural basis for understanding its unique interaction with beta-2 microglobulin (beta2m) and peptide. Consistent with the biological data that show an unusually weak association of Ld with beta2m, a novel orientation of the alpha1/alpha2 domains of Ld relative to beta2m results in a dearth of productive contacts compared with other class I proteins. Characteristics of the Ld antigen-binding cleft determine the unique motif of peptides that it binds. Ld has no central anchor residue due to the presence of several bulky side chains in its mid-cleft region. Also, its cleft is significantly more hydrophobic than that of the other class I molecules for which structures are known, resulting in many fewer H-bonds between peptide and cleft residues. The choice of Pro as a consensus anchor at peptide position 2 appears to be related to the hydrophobicity of the B pocket, and to the unique occurrence of Ile (which mirrors Pro in its inability to form H-bonds) at position 63 on the edge of this pocket. Thus, the paucity of stabilizing H-bonds combined with poor complementarity between peptide postion 2 Pro and the B pocket contribute to the weak association between Ld and its peptide antigen. The unique structural interactions of Ld with beta2m and peptide could make Ld more suited than other classical class I molecules to play a role in alternative pathways of antigen presentation.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS I H-2LD HEAVY CHAIN
A, D
268Mus musculusGene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2 MICROGLOBULIN
B, E
99Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NANO-PEPTIDE
C, F
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 150.100α = 90.00
b = 87.200β = 90.00
c = 80.300γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
XENGENdata scaling
X-PLORrefinement
XENGENdata reduction
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance